Re: Did Baltar know Ellen Tigh was a cylon?
There's no real reason to suppose that the final five were physically special; it was their technology and seemingly their genetic pool that created the significant seven models. Also, Baltar's cylon detector (mark two) works by simply identifying synthetic samples from natural ones, or so he tells Adama. Barring a substantial plot hole, a false negative result or a completely out-of-character decision to sabotage the test and let potentially crucial information pass by him, Baltar knew perfectly well that Ellen was a cylon.
It's probably just a plot hole, though.
"Two things have always been true about human beings. One, the world is always getting better. Two, the people living at that time think it`s getting worse."